This directory contains alignments of the zebrafish assembly
(danRer1, Nov. 2003) to the mouse assembly (mm5, May 2004)
in "axt" format. For a description, see
http://genome.ucsc.edu/goldenPath/help/axt.html.
The alignments were produced by the blastz alignment program, which
is available from Webb Miller's lab at Penn State University
(http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was:
A C G T
A 91 -90 -25 -100
C -90 100 -100 -25
G -25 -100 100 -90
T -100 -25 -90 91
with a gap open penalty of 400 and a gap extension penalty of 30. The
minimum score for an alignment to be kept was 6000 for the first pass
and 2000 for the second pass, which restricted the search space to the
regions between two alignments found in the first pass.
Each chromosome was divided into 10,000,000 base chunks for the blastz
alignments and all repeats for each organism were used as lineage-specific
repeats. Repeats were detected with Arian Smit's RepeatMasker program
using a zebrafish repeats library. The .lav format blastz output, which
does not include the sequence, was converted to .axt with lavToAxt. Low
scores can occur using the scoring matrix above and with repeats
abridged; therefore, alignments were rescored using PSU's restore_rpts
program and the default scoring matrix:
A C G T
A 91 -114 -31 -123
C -114 100 -125 -31
G -31 -125 100 -114
T -123 -31 -114 91
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If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to
the directory goldenPath/mm5/vsDanRer1/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the files in this directory are freely usable for any purpose.
All zebrafish sequence data are made available before scientific
publication with the understanding that the groups involved in generating
the data intend to publish the initial large-scale analyses of the dataset.
This will include a summary detailing the data that have beeen generated
and key features of the genome identified from genomic assembly and clone
mapping/sequencing. Any redistribution of the data should carry this notice.
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References
Chiaromonte, F., Yap, V.B., and Miller, W. Scoring pairwise genomic
sequence alignments. Pac Symp Biocomput 2002;115-26.
Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.
Evolution's cauldron: Duplication, deletion, and rearrangement in the
mouse and human genomes. Proc Natl Acad Sci USA 100(20):11484-11489
Sep 30 2003.
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,
Haussler, D., and Miller, W. Human-mouse alignments with BLASTZ</A>.
Genome Res. 13(1):103-7 (2003).
Name Last modified Size Description
Parent Directory -
md5sum.txt 2004-09-10 22:27 2.1K
chrY_random.axt.gz 2004-08-02 19:27 18K
chrY.axt.gz 2004-08-02 19:27 6.8M
chrX_random.axt.gz 2004-08-02 19:27 793K
chrX.axt.gz 2004-08-02 19:27 16M
chrUn_random.axt.gz 2004-08-02 19:27 89M
chrM.axt.gz 2004-08-02 19:26 15K
chr19_random.axt.gz 2004-08-02 19:22 1.2M
chr19.axt.gz 2004-08-02 19:22 6.7M
chr18_random.axt.gz 2004-08-02 19:22 110K
chr18.axt.gz 2004-08-02 19:22 8.4M
chr17_random.axt.gz 2004-08-02 19:22 123K
chr17.axt.gz 2004-08-02 19:22 31M
chr16_random.axt.gz 2004-08-02 19:21 33K
chr16.axt.gz 2004-08-02 19:21 6.2M
chr15_random.axt.gz 2004-08-02 19:21 14K
chr15.axt.gz 2004-08-02 19:21 17M
chr14_random.axt.gz 2004-08-02 19:20 156K
chr14.axt.gz 2004-08-02 19:20 6.4M
chr13_random.axt.gz 2004-08-02 19:20 37K
chr13.axt.gz 2004-08-02 19:20 16M
chr12_random.axt.gz 2004-08-02 19:20 129K
chr12.axt.gz 2004-08-02 19:20 8.4M
chr11.axt.gz 2004-08-02 19:20 12M
chr10_random.axt.gz 2004-08-02 19:20 31K
chr10.axt.gz 2004-08-02 19:20 8.9M
chr9_random.axt.gz 2004-08-02 19:26 36K
chr9.axt.gz 2004-08-02 19:26 21M
chr8_random.axt.gz 2004-08-02 19:25 42K
chr8.axt.gz 2004-08-02 19:25 9.9M
chr7_random.axt.gz 2004-08-02 19:25 8.9M
chr7.axt.gz 2004-08-02 19:25 54M
chr6_random.axt.gz 2004-08-02 19:24 102K
chr6.axt.gz 2004-08-02 19:24 18M
chr5_random.axt.gz 2004-08-02 19:24 171K
chr5.axt.gz 2004-08-02 19:24 17M
chr4_random.axt.gz 2004-08-02 19:23 806K
chr4.axt.gz 2004-08-02 19:23 13M
chr3_random.axt.gz 2004-08-02 19:23 129K
chr3.axt.gz 2004-08-02 19:23 12M
chr2_random.axt.gz 2004-08-02 19:23 1.5M
chr2.axt.gz 2004-08-02 19:23 32M
chr1_random.axt.gz 2004-08-02 19:22 46K
chr1.axt.gz 2004-08-02 19:22 13M